We review the definition of hypergroups by Sunder, and we associate a hypergroup to a type III subfactor $N\subset M$ of finite index, whose canonical endomorphism $\gamma\in\mathrm{End}(M)$ is multiplicity-free. It is realized by positive maps of $M$ that have $N$ as fixed points. If the depth is $>2$, this hypergroup is different from the hypergroup associated with the fusion algebra of $M$-$M$ bimodules that was Sunder's original motivation to introduce hypergroups. We explain how the present hypergroup, associated with a suitable subfactor, controls the composition of transparent boundary conditions between two isomorphic quantum field theories, and that this generalizes to a hypergroupoid of boundary conditions between different quantum field theories sharing a common subtheory.